the gencode pseudogene resource的gencode假基因资源.pdfVIP

Pei et al. Genome Biology 2012, 13:R51 /2012/13/9/R51 RESEARCH Open Access The GENCODE pseudogene resource 1† 1,2† 3 4 1 1 Baikang Pei , Cristina Sisu , Adam Frankish , Cédric Howald , Lukas Habegger , Xinmeng Jasmine Mu , 5 1,2 6 5 4 Rachel Harte , Suganthi Balasubramanian , Andrea Tanzer , Mark Diekhans , Alexandre Reymond , Tim J Hubbard3, Jennifer Harrow3 and Mark B Gerstein1,2,7* Abstract Background: Pseudogenes have long been considered as nonfunctional genomic sequences. However, recent evidence suggests that many of them might have some form of biological activity, and the possibility of functionality has increased interest in their accurate annotation and integration with functional genomics data. Results: As part of the GENCODE annotation of the human genome, we present the first genome-wide pseudogene assignment for protein-coding genes, based on both large-scale manual annotation and in silico pipelines. A key aspect of this coupled approach is that it allows us to identify pseudogenes in an unbiased fashion as well as untangle complex events through manual evaluation. We integrate the pseudogene annotations with the extensive ENCODE functional genomics information. In particular, we determine the expression level, transcription-factor and RNA polymerase II binding, and chromatin marks associated with each pseudogene. Based on their distribution, we develop simple statistical models for each type of activity, which we validate with large- scale RT-PCR-Seq experiments. Finally, we compare our pseudogenes with conservation and variation data from prim